feat: add package extension for OrdinaryDiffEq (#150)

AlgebraicJulia · May 23, 2023 · 5d12a7a · 5d12a7a
1 parent 856d763
commit 5d12a7a
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Showing 5 changed files with 34 additions and 5 deletions.
diff --git a/Project.toml b/Project.toml
@@ -13,12 +13,14 @@ LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 [weakdeps]
 Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Petri = "4259d249-1051-49fa-8328-3f8ab9391c33"
 
 [extensions]
-AlgebraicPetriPetriExt = "Petri"
 AlgebraicPetriCatalystExt = "Catalyst"
 AlgebraicPetriModelingToolkitExt = "ModelingToolkit"
+AlgebraicPetriOrdinaryDiffEqExt = "OrdinaryDiffEq"
+AlgebraicPetriPetriExt = "Petri"
 
 [compat]
 Catalyst = "13"
@@ -27,5 +29,6 @@ DataStructures = "0.18"
 GeneralizedGenerated = "0.3"
 LabelledArrays = "1"
 ModelingToolkit = "8"
+OrdinaryDiffEq = "6"
 Petri = "1"
 julia = "1.9"
diff --git a/ext/AlgebraicPetriOrdinaryDiffEqExt.jl b/ext/AlgebraicPetriOrdinaryDiffEqExt.jl
@@ -0,0 +1,9 @@
+module AlgebraicPetriOrdinaryDiffEqExt
+
+using AlgebraicPetri
+import OrdinaryDiffEq: ODEProblem
+
+ODEProblem(m::AbstractPetriNet, u0, tspan, β) = ODEProblem(vectorfield(m), u0, tspan, β)
+ODEProblem(m::AbstractPetriNet, tspan) = ODEProblem(vectorfield(m), concentrations(m), tspan, rates(m))
+
+end
diff --git a/src/AlgebraicPetri.jl b/src/AlgebraicPetri.jl
@@ -13,7 +13,7 @@ export SchPetriNet, PetriNet, OpenPetriNetOb, AbstractPetriNet, ns, nt, ni, no,
   Open, OpenPetriNet, OpenLabelledPetriNet, OpenReactionNet, OpenLabelledReactionNet,
   OpenPetriNetOb, OpenLabelledPetriNetOb, OpenReactionNetOb, OpenLabelledReactionNetOb,
   mca, flatten_labels,
-  AbstractPropertyPetriNet, sprop, tprop, sprops, tprops,
+  AbstractPropertyPetriNet, AbstractPropertyReactionNet, sprop, tprop, sprops, tprops,
   SchPropertyPetriNet, SchPropertyLabelledPetriNet, SchPropertyReactionNet, SchPropertyLabelledReactionNet,
   PropertyPetriNet, PropertyLabelledPetriNet, PropertyReactionNet, PropertyLabelledReactionNet,
   OpenPropertyPetriNet, OpenPropertyLabelledPetriNet, OpenPropertyReactionNet, OpenPropertyLabelledReactionNet,
@@ -558,7 +558,7 @@ See Catlab.jl documentation for description of the @present syntax.
   sname::Attr(S, Name)
 end
 
-@abstract_acset_type AbstractLabelledReactionNet <: AbstractPetriNet
+@abstract_acset_type AbstractLabelledReactionNet <: AbstractReactionNet
 @acset_type LabelledReactionNetUntyped(SchLabelledReactionNet, index=[:it, :is, :ot, :os]) <: AbstractLabelledReactionNet
 const LabelledReactionNet{R,C} = LabelledReactionNetUntyped{R,C,Symbol}
 const OpenLabelledReactionNetObUntyped, OpenLabelledReactionNetUntyped = OpenACSetTypes(LabelledReactionNetUntyped, :S)
@@ -736,7 +736,8 @@ See Catlab.jl documentation for description of the @present syntax.
   sprop::Attr(S, Prop)
   tprop::Attr(T, Prop)
 end
-@acset_type PropertyReactionNet(SchPropertyReactionNet, index=[:it, :is, :ot, :os]) <: AbstractPropertyPetriNet
+@abstract_acset_type AbstractPropertyReactionNet <: AbstractPropertyPetriNet
+@acset_type PropertyReactionNet(SchPropertyReactionNet, index=[:it, :is, :ot, :os]) <: AbstractPropertyReactionNet
 
 const OpenPropertyReactionNetOb, OpenPropertyReactionNet = OpenACSetTypes(PropertyReactionNet, :S)
 Open(p::PropertyReactionNet{R,C,T}, legs...) where {R,C,T} = OpenPropertyReactionNet{R,C,T}(p, map(l -> FinFunction(l, ns(p)), legs)...)
@@ -752,7 +753,7 @@ See Catlab.jl documentation for description of the @present syntax.
   sprop::Attr(S, Prop)
   tprop::Attr(T, Prop)
 end
-@acset_type PropertyLabelledReactionNetUntyped(SchPropertyLabelledReactionNet, index=[:it, :is, :ot, :os]) <: AbstractPropertyPetriNet
+@acset_type PropertyLabelledReactionNetUntyped(SchPropertyLabelledReactionNet, index=[:it, :is, :ot, :os]) <: AbstractPropertyReactionNet
 const PropertyLabelledReactionNet{R,C,T} = PropertyLabelledReactionNetUntyped{R,C,Symbol,T}
 
 const OpenPropertyLabelledReactionNetObUntyped, OpenPropertyLabelledReactionNetUntyped = OpenACSetTypes(PropertyLabelledReactionNetUntyped, :S)

diff --git a/test/Project.toml b/test/Project.toml
@@ -5,6 +5,7 @@ Catalyst = "479239e8-5488-4da2-87a7-35f2df7eef83"
 Catlab = "134e5e36-593f-5add-ad60-77f754baafbe"
 LabelledArrays = "2ee39098-c373-598a-b85f-a56591580800"
 ModelingToolkit = "961ee093-0014-501f-94e3-6117800e7a78"
+OrdinaryDiffEq = "1dea7af3-3e70-54e6-95c3-0bf5283fa5ed"
 Petri = "4259d249-1051-49fa-8328-3f8ab9391c33"
 Tables = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
diff --git a/test/ext/AlgebraicPetriOrdinaryDiffEqExt.jl b/test/ext/AlgebraicPetriOrdinaryDiffEqExt.jl
@@ -0,0 +1,15 @@
+module TestAlgebraicPetriOrdinaryDiffEqExt
+
+using Test
+using AlgebraicPetri
+using OrdinaryDiffEq
+
+sir_petri = PetriNet(3, ((1, 2), (2, 2)), (2, 3))
+sir_rxn = ReactionNet{Number,Int}([990, 10, 0], (0.001, ((1, 2) => (2, 2))), (0.25, (2 => 3)))
+
+sol_petri = solve(ODEProblem(sir_petri, [990, 10, 0], (0,100.0), [0.001, 0.25]), Tsit5())
+sol_rxn = solve(ODEProblem(sir_rxn, (0,100.0)), Tsit5())
+
+@test sol_petri.u == sol_rxn.u
+
+end